Custom brushes not saved
I finally figured out why the icon paths are being lost, follow all the steps you're doing so far and then;

Save the blend file to where your custom brush Icons folder is (in my case I am modifying my startup file so I've put my custom brush Icons folder into %APPDATA%\Blender Foundation\Blender\2.90\config)
Then do File &gt; External Data &gt; Make All Paths Absolute.